Are you connecting via wireless by chance?
I had an issue very similar to this a while back where Filezilla would work but DW wouldn't. It turned out to be an issue with my wireless router. I was able to connect directly to my modem (they were separate units) and connect without issue. I was also able to connect without issue in DW from other networks. I replaced my wireless and the problem has never come back.
Admittedly, it's a long shot, but may be worth checking your hardware.
